Social insect colonies are based on a reproductive division of labor in which only one or a few individuals specialize in reproduction. However, within this general framework, social insect species exhibit considerable diversity in colony breeding structure, with termites showing the most variation. Termites are therefore an excellent group for investigating the historical and ecological factors shaping colony breeding structure. The last decade has seen tremendous progress in our understanding of colony breeding structure in termites, buoyed in large part by the application of molecular genetic markers. There are three main components of colony breeding structure in termites: 1.) the number of breeding individuals (males and females), 2.) the degree of relatedness among the breeders, 3.) and whether the breeders are primary reproductives or neotenics (immature, non-alate derived). While each of these components can vary independent of the others, in general they tend to be closely associated, with the presence of multiple reproductives usually occurring in the form of inbred neotenics who replace the founding king and queen. Breeding structure is strongly influenced by both phylogeny and ecology. These trends will be reviewed in light of recent data from molecular studies. Finally, constraints on inbreeding in termite colonies will be discussed.